Index

A

add_continuous_colorbar() (in module mdsa_tools.Viz) add_discrete_colorbar() (in module mdsa_tools.Viz)

assignment_schemas() (mdsa_tools.Analysis.systems_analysis method) autocorrelation_function() (mdsa_tools.Analysis.systems_analysis method)

B

bubble_grid_manifoldlearning() (in module mdsa_tools.Viz)

C

cluster_embeddingspace() (mdsa_tools.Analysis.systems_analysis method) compute_cluster_assignment_schemas() (mdsa_tools.Analysis.systems_analysis method) contour_embedding_space() (in module mdsa_tools.Viz) cpptraj_hbond_import (class in mdsa_tools.Cpptraj_import) create_2d_color_mappings() (in module mdsa_tools.Viz)

create_attributes() (mdsa_tools.Data_gen_hbond.TrajectoryProcessor method) create_filtered_representations() (mdsa_tools.Data_gen_hbond.TrajectoryProcessor method) create_MDcircos_from_weightsdf() (in module mdsa_tools.Viz) create_PCA_ranked_weights() (mdsa_tools.Analysis.systems_analysis method) create_system_representations() (mdsa_tools.Data_gen_hbond.TrajectoryProcessor method) create_transition_probability_matrix() (mdsa_tools.subdomain_explorations.subdomain_explorations method)

E

edgelist_single_frame() (mdsa_tools.Cpptraj_import.cpptraj_hbond_import method) evaluate_cohesion_shrinkingwindow() (mdsa_tools.subdomain_explorations.subdomain_explorations method) evaluate_cohesion_slidingwindow() (mdsa_tools.subdomain_explorations.subdomain_explorations method)

extract_hbond_values() (mdsa_tools.Analysis.systems_analysis method) extract_headers() (mdsa_tools.Cpptraj_import.cpptraj_hbond_import method) extract_properties_from_weightsdf() (in module mdsa_tools.Viz)

G

get_Circos_coordinates() (in module mdsa_tools.Viz)

I

iterate_frames() (mdsa_tools.Cpptraj_import.cpptraj_hbond_import method)

L

lookup_table_from_edgelist() (mdsa_tools.Cpptraj_import.cpptraj_hbond_import method)

M

make_MDCircos_object() (in module mdsa_tools.Viz) mdcircos_graph() (in module mdsa_tools.Viz) mdsa_tools.Analysis module mdsa_tools.Cpptraj_import module mdsa_tools.Data_gen_hbond module mdsa_tools.subdomain_explorations module

mdsa_tools.Viz module module mdsa_tools.Analysis mdsa_tools.Cpptraj_import mdsa_tools.Data_gen_hbond mdsa_tools.subdomain_explorations mdsa_tools.Viz

P

pearson_sums_only() (mdsa_tools.Analysis.systems_analysis method) perform_clust_opt() (mdsa_tools.Analysis.systems_analysis method) perform_kmeans() (mdsa_tools.Analysis.systems_analysis method) perform_optimized_UMAP_global() (mdsa_tools.Analysis.systems_analysis method)

perform_optimized_UMAP_local() (mdsa_tools.Analysis.systems_analysis method) plot_elbow_scores() (in module mdsa_tools.Viz) plot_sillohette_scores() (in module mdsa_tools.Viz) Process_trajectory() (mdsa_tools.Data_gen_hbond.TrajectoryProcessor method)

R

reduce_systems_representations() (mdsa_tools.Analysis.systems_analysis method) replicatemap_from_labels() (in module mdsa_tools.Viz) replicates_to_feature_matrix() (mdsa_tools.Analysis.systems_analysis method)

rmsd_from_centers() (mdsa_tools.subdomain_explorations.subdomain_explorations method) rmsd_lineplots() (in module mdsa_tools.Viz) run_PCA() (mdsa_tools.Analysis.systems_analysis method)

S

set_ticks() (in module mdsa_tools.Viz)

subdomain_explorations (class in mdsa_tools.subdomain_explorations) systems_analysis (class in mdsa_tools.Analysis)

T

t_test_autocorrelation() (mdsa_tools.Analysis.systems_analysis method)

TrajectoryProcessor (class in mdsa_tools.Data_gen_hbond)

V

visualize_reduction() (in module mdsa_tools.Viz)